SimulateFreeEnergy

SimulateFreeEnergy[reaction, temperature]⟹freeEnergyObject

computes the free energy of the given reaction between two nucleic acid oligomers at the specified concentration with traditional Nearest Neighbor thermodynamic analysis.

SimulateFreeEnergy[reactantAplusB, temperature]⟹freeEnergyObject

finds the product of reaction from 'reactantA' + 'reactantB', then computes the free energy.

SimulateFreeEnergy[reactantEquilibriumProduct, temperature]⟹freeEnergyObject

infers the type of reaction from the given 'reactant' ⇌ 'product' state and computes the free energy for that reaction.

SimulateFreeEnergy[reactionMechanism, temperature]⟹freeEnergyObject

computes the free energy from the reaction in the given mechanism.

SimulateFreeEnergy[oligomer, temperature]⟹freeEnergyObject

considers the hybridization reaction between the given oligomer and its reverse complement.

SimulateFreeEnergy[structure, temperature]⟹freeEnergyObject

considers the melting reaction whereby all of the bonds in the given structure are melted.

SimulateFreeEnergy[enthalpy, entropy, temperature]⟹freeEnergyObject

computes the free energy from the given enthalpy and entropy of a reaction.

Details

Free energy is calculated from ΔG = ΔH - T ΔS.
DNA Nearest Neighbor parameters from Object[Report, Literature, "id:kEJ9mqa1Jr7P"]: Allawi, Hatim T., and John SantaLucia. "Thermodynamics and NMR of internal GT mismatches in DNA." Biochemistry 36.34 (1997): 10581-10594.
RNA Nearest Neighbor parameters from Object[Report, Literature, "id:M8n3rxYAnNkm"]: Xia, Tianbing, et al. "Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs." Biochemistry 37.42 (1998): 14719-14735.
If given a nucleic acid sequence, strand, or sequence length, this function assumes a two-state binding between the provided sequence and a perfect reverse complement.
Given a structure, considers only the bonded regions of the structure.
Supported polymer types are DNA and RNA.
Untyped sequences or lengths default to DNA if there is ambiguity.
Enthalpy is independent of salt concentration, while entropy values for a given salt concentration. MonovalentSaltConcentration and DivalentSaltConcentration can be used to specify the concentration of monovalent salt (Na+, K+) and divalent salt (Mg2+) respectively. The entropy correction term is calculated as: 0.368*(Sequence Length - 1)*ln[(Na+) + 140*(Mg2+)] from Object[Report,Literature, "id:eGakld09nLXo"]: von Ahsen, et al. "Application of a Thermodynamic Nearest-Neighbor Model to Estimate Nucleic Acid Stability and Optimize Probe Design:Prediction of Melting Points of Multiple Mutations of Apolipoprotein B-3500 and Factor V with a Hybridization Probe Genotyping Assay on the LightCycler" Clinical Chemistry 45.12 (1999) 2094-2101.
Temperature defaults to 37.0 °C.

Input

Output

General Options

Examples

Basic Examples (5)

Compute the Gibbs free energy of a hybridization reaction between given sequence and its reverse complement:

Find the product of DNA['GGACTGACGCGTTGA']+DNA['TCAACGCGTCAGTCC'], then compute the Gibbs free energy:

Specify reaction from one structure to another:

Compute the Gibbs free energy from entropy and enthalpy:

Additional Examples (18)

Input temperature as a distribution:

Input enthalpy, entropy and temperature as distributions:

Compute the free energy from a simple ReactionMechanism contains only one reaction:

Pull strand from given sample:

Pull strand from given model:

Given reaction model:

Given structure, computes free energy of all bonded regions:

Compute the distribution of free energy of all 15-mer hybridization reactions with their reverse complements:

Specify a temperature:

Given a strand:

Given a typed sequence:

Given untyped length:

Temperature defaults to 37 Celsius:

Structure with no bonds returns zero:

Can handle degenerate sequence and return a distribution:

Return free energy distribution instead of mean:

Return free energy of a structure for which the thermodynamic parameters for mismatch is not available:

Options (9)

AlternativeParameterization (1)

Using AlternativeParameterization to specially useful if there is no thermo properties in the original polymer:

BufferModel (1)

Specify a specific buffer, from which salt concentration will be computed:

DivalentSaltConcentration (1)

Specify divalent salt concentration in buffer:

MonovalentSaltConcentration (1)

Specify monovalent salt concentration in buffer:

Polymer (1)

Specify polymer for untyped sequences:

ReactionType (1)

Given an object, specify if the strands should be hybridized or the structure melted:

Template (2)

The Options from a previous free energy simulation (object reference) can be used to preform an identical simulation on new oligomer:

The Options from a previous free energy simulation (object) can be used to preform an identical simulation on new oligomer:

ThermodynamicsModel (1)

Using ThermodynamicsModel to explicitly provide the thermodynamic parameters or to override the values taken from Thermodynamics field in the model oligomer: